How to keep your Microbes Happy!

With The Herbal Clinic - Swansea

Discovering the complexity of the life forms living within us and what they mean to our health has generated a massive surge of interest amongst the scientific community. This interest has rippled into the lives of those wishing to maintain their own wellbeing, as yet the research is still in its infancy.

However, it is not necessary to know exactly which microbes are present within, to be able to care for your own beneficial microscopic community. Much like tending a garden, we do not need to understand all the minibeasts that live in the soil to cultivate a space of harmony – though it may be interesting to study them!

A flourishing inner landscape requires we pay attention to what we put in; clean air, water and quality nutrients. Our inner gardeners (the digestive organs) need to do the work necessary to process these and the wastes must be removed to prevent attracting unwanted guests. Tend to yourself as you would your garden and both your microbiome and you will be happy and vital.

The Gruesome Essentials of Elimination

In our society of excess and toxicity, it is usually most necessary to work on improving the removal, or elimination of the body wastes. There are 4 primary systems of elimination (with a 5th system operating in women) and all of these have an important role to play. Signs that these systems are not functioning well should be heeded – if we deal with issues promptly we can prevent disease from developing.

  1. Lungs and respiratory system: The lining of the lungs is the first line of defence against inhaled particles. These are eliminated with the help of tiny hair like structures which beat to propel mucus upwards and out in a system known as the ‘mucociliary escalator’. Recurring colds or mucus production are a sign that the lungs may need some assistance. Sinusitis is also a superficial indication of what is happening in the lungs.
  2. Kidneys and Urinary system: The kidneys filter the waste products of the body – excess water and salts, particles left behind in the digestive system as well as drugs and toxins. This is all dealt with by the kidneys and excreted in the urine. Not only are recreational drugs harmful to the kidneys but also many prescription medications, some of which are heartburn drugs, antibiotics and painkillers. Urinary urgency, frequency or regularly needing to go to the toilet during the night are signs of an imbalance or weakness in the kidneys.
  3. Bowel: Lack of clearance creates stagnation, which allows the growth of unwanted bacteria. Bloating, irregular bowel movements and abdominal pains are suggestive of bowel dysfunction. The bowels should be emptied at least once per day.
  4. Skin: Sweating allows the release of toxins through the skin; unpleasant odours from the armpits and feet are a sign that these are not eliminating effectively. Acne and other inflammatory skin conditions, like psoriasis can also be triggered by lack of clearance through the sweat. Antiperspirant deodorants prevent this form of elimination, blocking an area in which the lymphatic fluid drains carrying toxic wastes from the body to be eliminated through the sweat glands. Incidentally, it is the top outer corner of the breast tissue that is primarily affected in breast cancers2; some studies have found a link between underarm shaving followed by the application of anti-perspirant deodorant and earlier onset of breast cancer.
  5. Uterus: The uterus is an additional system of elimination in females. Signs that the uterus is not clearing effectively include heavy, painful, absent or irregular periods as well as those of long duration and clotting. Most negative symptoms associated with menstruation are as a result of the system not eliminating well.

Toxic Checklist

How many of these are in your life on a daily basis? With such a long list it’s easy to see why even if we try to live ‘cleanly’, our systems may still suffer from some overload.

  • Drugs (pharmaceutical or recreational)
  • Chlorine from tap water
  • Pesticides and herbicides2 from inorganic produce (heavily contaminated crops include wheat, soybeans and corn.)
  • Chemical food additives and preservatives
  • Mattressess with PBDEs
  • Chemical cleaning products
  • Make up and perfume
  • Air fresheners
  • Plastic food and drinks containers
  • Antiperspirant deodorants
  • Fabric softeners
  • Non-stick cookware
  • Canned foods
  • Mobile phones

4 Ways to Nourish your Gut Microbiome

Eat more veg! There’s often no need to change what you eat, just adjust the quantities. Select a variety of vegetables that you enjoy, include vegetables in dishes that you usually prepare without and work your way towards 70% vegetables (including some fruit) of your overall food intake. They provide fibre and prebiotics which feed the beneficial bacteria, one of the simplest ways to nourish your gut microbiome.

Include fermented foods. Historically fermentation was used by our ancestors to preserve foods in days when there was no access to refrigeration and now we’ve realised that fermented foods help increase the microbial diversity of the gut. There are plenty to choose from – try making your own sauerkraut (see The Herbal Clinics ‘posts’ section online for a simple recipe); pick up some kefir or kombucha and see how it makes your digestion feel. You may notice a lively ‘awakened’ feeling in the gut giving you an overall energised sensation. Not everyone finds fermented foods beneficial. Tune into your own digestion and see if they suit you.

Drink filtered water. The chlorine in water is there to destroy microbial life. Your microflora won’t thank you for it!

Fasting. Short term fasting has been linked to reduced inflammation, increased lifespan and re-duced aging with less chronic disease. In addition, fasting can result in reduced gut permeability (helping to heal leaky gut) and although there has been little research so far, what there is finds a positive effect on the gut microbiome. Take the plunge and experiment with fasting.

Note: Fasting is not advisable with some health conditions and during pregnancy. Consult a health practitioner for guidance.

The Changing Microbiome


Before birth we are sterile – we have no microbes; at the moment we enter the world microbes colonise our bodies. During pregnancy the microbes in the birth canal change becoming ideally suited for the babies first microbial residents. Babies delivered by C-section are colonised primarily by skin microbes, a very different species which can result in increased susceptibility to infection. Some parents of babies born in this way are using ‘swabbing’ as a way to introduce the more favourable bacteria from the outset.

1 Day to 6 Months

Young babies pick up microbes from their family members and surroundings. The food babies eat will affect their microbial balance and those who drink breast milk will have different gut microbes from those who are given formula.

6 Months to 3 Years

Microbial populations change significantly in early childhood and as children develop the early similarity to their mother’s microbiome shifts and they begin to more equally resemble the father and mother. Events such as a fever, new foods or antibiotics can cause sudden shifts in the bacteria with changes that may last for years or even life.

3 Years to Adult

By 3 years a child’s microbiome is much more stable and this continues into adulthood. Major hormonal changes that occur during puberty, pregnancy and menopause can all result in changes to the microbiome, so for example the increase in oil secretion by the skin during puberty encourages the growth of a different type of bacteria.


After the age of 65 years there is a gradual shift in the microbiome with the number of species reducing and a distinct profile emerging. There is often a decline in beneficial species and this altered flora is associated with frailty in the elderly1. Do not despair! These changes are linked to lifestyle and diet shifts, as well as issues such as reduced gastric acid secretion and impaired absorption which then affects nutritional levels. These are all matters which can be addressed and resolved with proper care and attention. At The Herbal Clinic we have patients in their 80s and 90s with as much zest for life as a 30 year old, advancing age is not a ticket to decline!

The Herbal Clinic – Meilyr James

32 King Edward Road, Swansea SA1 4LL

01792 474356

  1. Claesson MJ, et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 2011; 108 Suppl 1:4586-91; PMID:20571116
  2. Samsel A, Seneff S (2013) Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases. Entropy 2013, 15(4), 1416-1463; doi:10.3390/e15041416.




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